An organ was first played at Gloria Dei in 1703 at the ordination of Justus Falckner (the first protestant clergyman ordained in America). By virtue of this event, Gloria Dei has the distinction of being the first church in Colonial America where an organ was used. Several organs are known to have been installed in the church in the 19th century.

The present Hook and Hastings of Boston instrument (#1981) was commissioned in 1902 and has served the congregation well since then.

The organ is larger than the building requires because Hook and Hastings designed it to showcase their product in the Philadelphia region.

At that time, Hook and Hastings was one of the most respected organ builders in the country and several dozens of their organs were eventually purchased in Philadelphia, many of which have since been discarded, burned or neglected. The Gloria Dei instrument was fully restored in 1992 by R.J. Brunner and Co. of Silver Springs, PA.

The organ has 27 ranks - about 1300 pipes. It is controlled by three sets of keyboards - the swell, the great and the pedals. During the recent restoration, tonal additions were made in keeping with the style and spirit of the instrument. The most ambitious element of the restoration was the addition of an electronic combination action, enabling the organist to make quick sound changes without an assistant.